Zuzanna Jakubowska

The protein kinase-like (PKL) superfamily regulates metabolism, biofilm formation, host interactions, and antimicrobial resistance in bacteria, although much of its diversity remains unknown. We used a structure-based pipeline that combined protein structure prediction with structural similarity searches to search 5.1 million protein sequences in the Human Oral Microbiome Database (HOMD). Together with 30 families that had been previously characterized, we identified 20 PKL families new to this genome collection: 15 entirely novel and 5 previously reported as preliminary findings. Our taxonomic analysis revealed that the families were distributed either across multiple bacterial phyla or restricted to a single species; hits spanning domains suggest either ancient origins or horizontal transfer. Three families were examined in detail and show different evolutionary pathways: SEAE1 from Segetibacter aerophilus , which is a putative lipid kinase; POGI1 from Porphyromonas gingivalis , a putative ethanolamine kinase with the PKL fold that is limited to pathogens; and SrfA-N from Haemophilus parainfluenzae , a non-catalytic scaffold that has been convergently co-opted as a tripartite toxin platform. Taken together, these examples demonstrate enzymatic specialization, adaptation specific to pathogens and structural co-option. The families identified are candidates for further mechanistic study.

An important component of sustainable agriculture is the development of strategies that reduce the use of mineral fertilizers while maintaining high crop productivity. One promising approach is the application of plant growth-promoting bacteria (PGPB), which may support plant development and improve nutrient use efficiency. A field experiment with winter wheat was conducted in south-western Poland during two growing seasons, 2023–2024 and 2024–2025, to evaluate the effect of inoculation with Priestia sp. KR219 under different nitrogen fertilization regimes. The experiment included three levels of nitrogen: 70, 91, and 130 kg N ha⁻¹ (54%, 70%, and 100% of the full spring nitrogen fertilization rate) with and without bacterial application. Soil chemical and biological properties, photosynthetic pigment content, plant morphological traits, grain yield, as well as grain chemical composition and amino acid profile were evaluated. The inoculated treatments showed higher soil dehydrogenase activity in the second growing season and higher contents of selected photosynthetic pigments, particularly chlorophyll a, under reduced nitrogen fertilization. Bacterial inoculation was also associated with numerical increases in grain yield in most treatment combinations, although these differences were not statistically significant. Differences among treatment combinations involving nitrogen fertilization were more pronounced for grain chemical composition and amino acid profile than differences between inoculated and non-inoculated treatments at the same nitrogen level, with the full nitrogen rate generally resulting in the highest protein content and higher contents of several essential and non-essential amino acids. Overall, the responses observed following Priestia sp. KR219 inoculation included changes in selected soil and physiological parameters, while responses in grain yield and quality varied between growing seasons. Further studies under diverse environmental conditions are required to determine its agronomic potential.

Chlorophylls and carotenoids are key plant metabolites involved in photosynthesis, stress responses, and antioxidant activity. This study aimed to examine intrapopulation variability in Melica uniflora Retz. (wood melick), focusing on chlorophyll and carotenoid content in relation to the developmental stage and environmental conditions. Research was carried out over three consecutive years (2021–2023) in the Ślęża Massif near Sobótka, Lower Silesia, Poland. Leaf blades samples were collected annually from ten natural forest sites at two time points: summer (July) and autumn (October), and analyzed for chlorophyll a, chlorophyll b, and total carotenoids using spectrophotometry. Statistical analyses, including ANOVA, were used to assess the effects of year, harvest time, and site on pigment concentrations. The average (±SD) pigment content in M. uniflora was 1.44 ± 0.73 mg∙g⁻¹ DM for chlorophyll a, 0.67 ± 0.40 mg∙g⁻¹ DM for chlorophyll b, and 0.46 ± 0.28 mg∙g⁻¹ DM for total carotenoids. Among the factors studied, year and developmental stage had the strongest statistically significant influence on chlorophyll and carotenoid levels, while site-specific differences contributed to intrapopulation variability to a lesser extent (p < 0.001). Interestingly, the first year of the study showed higher average pigment levels across both harvest times. Summer-collected plants had higher concentrations of all pigments than those collected in autumn. Differences among sites further indicated intrapopulation variability within this species. These findings provide new insights into the natural variability of photosynthetic metabolites in forest grasses and may serve as a reference for studies on the adaptive and biochemical responses of woodland plant species to environmental factors.

Pseudomonas protegens, a member of the P. fluorescens complex, is an important biocontrol agent with high potential in sustainable agriculture. It produces diverse secondary metabolites, including 2,4-diacetylphloroglucinol (DAPG), pyoluteorin (PLT), orfamides, and protegenins, as well as hydrolytic enzymes such as chitinases, which contribute to antifungal activity, fungal cell wall degradation, and induction of systemic resistance (ISR) in plants. Despite these insights, gaps remain in understanding the regulation of metabolite biosynthesis, variability of ISR across crops, and the field efficacy of P. protegens. Future research should employ omics approaches (metagenomics, transcriptomics) to optimize biocontrol strategies, explore natural inducers of metabolite production, and evaluate colonization efficiency under field conditions. This review synthesizes current knowledge on P. protegens, highlighting its importance, mechanisms of action, existing knowledge gaps, and directions for future research.

Biofortification of plants using Plant Growth-Promoting Bacteria (PGPB) represents a promising strategy in sustainable agriculture. This paper discusses the PGPB action in the context of their impact on phenolic compounds biosynthesis and the prospects for their application in agriculture. So far, no review article has summarized the significance of PGPB in increasing phenolic compounds in plants. PGPB, such as Pseudomonas, Bacillus, and Azospirillum, promote plant growth by producing phytohormones, enhancing nutrient availability, and stimulating the biosynthesis of secondary metabolites through the activation of Induced Systemic Resistance (ISR). The activation of ISR (Induced Systemic Resistance) by PGPB stimulates the phenylpropanoid pathway, which is the primary biosynthetic route for polyphenolic compounds, including phenolic acids and flavonoids, in plants. Studies indicate that PGPB may increase phenolic compounds content from 9% to over 200%, while simultaneously improving antioxidant activity. Through the secretion of phenolic compounds, PGPB also can mitigate abiotic stresses such as drought, salinity and heavy metal contamination. Among the phenolic compounds whose production in various plant parts can be stimulated by PGPB are flavonoids, such as quercetin, procyanidin B1, EGCG, and catechin, and phenolic acids, including caffeic acid, ferulic acid, and chlorogenic acid. Advancements in omics research will enable a more precise investigation of the impact of PGPB, including endophytic bacteria, on the biosynthetic pathways of phenolic compounds. In the future, this will translate into improved efficiency in stimulating the production of these compounds. Nevertheless, even now, the use of PGPB offers a sustainable alternative to genetic engineering, reducing reliance on chemical inputs in agriculture.

Oilseed rape is one of the most important oilseed crops, requiring high levels of nitrogen fertilization. Excessive nitrogen use, however, leads to numerous negative environmental impacts, spurring the search for sustainable, environmentally friendly alternatives to reduce reliance on mineral nitrogen fertilizers. One promising approach involves plant-growth-promoting bacteria (PGPB), which can support oilseed rape growth and lessen the need for traditional nitrogen fertilizers. This study evaluates a selected microbial consortium comprising bacterial isolates obtained from soil: Pseudomonas sp. G31 and Azotobacter sp. PBC2 (P1A). The applied PGPB significantly increased seed yield (a 27.12% increase) and, in the initial phase of the study, reduced the ammonium nitrogen content in the soil (a 20.18% decrease). Metataxonomic analyses were performed using Next-Generation Sequencing (NGS) technology by Illumina. Although P1A did not significantly affect alpha diversity, it altered the relative abundance of some dominant soil microorganisms. In the BBCH 75 phase, the P1A consortium increased the abundance of bacteria of Firmicutes phylum, including the genera Bacillus and Paenibacillus, which was considered a beneficial change. In summary, the Pseudomonas sp. G31 and Azotobacter sp. PBC2 consortium increased seed yield and was found to be part of the native rhizosphere community of oilseed rape, making it a promising candidate for commercialization.

Plant growth-promoting bacteria (PGPB) are among the most promising alternatives to mineral fertilizers. However, little is known about the effects of applied bacteria on the native microbiota, including the rhizobacterial community, which plays a crucial role in bacteria-plant interactions. Therefore, this study is aimed at assessing the effects of PGPB not only on plants but also, importantly, on the native rhizobacterial community of winter oilseed rape. The bacterial consortium, consisting of Pseudomonas sp. KR227 and Azotobacter PBC1 (P2A), slightly promoted plant growth, increasing the root weight by 21.95% and seed yield by 18.94%. This likely results from its ability to produce indole-3-acetic acid (IAA), solubilize phosphorus, and fix nitrogen, as indicated by a 35.76% increase in N-NH₄ and a 35.05% increase in available phosphorus (AP). The introduced PGPB altered the rhizobacterial community of rapeseed, increasing the relative abundance of the phylum Proteobacteria and the genus Pseudomonas while decreasing the relative abundance of phylum Verrucomicrobiota (3 weeks after inoculation). Moreover, Proteobacteria were positively correlated with AP, while Verrucomicrobiota were correlated with N-NH₄. At the genus level, Flavobacterium and Pseudomonas were positively correlated with AP, whereas Candidatus Udaeobacter showed a positive correlation with N-NH₄ and a negative correlation with pH. Importantly, the P2A consortium did not significantly affect the diversity of native rapeseed rhizobacteria. These findings suggest that the tested P2A consortium has potential as a biostimulant in rapeseed cultivation.

The nutritional value of green forage is a result of various pratotechnical practices, including fertilisation and harvest timing. Additionally, individual plant species present in natural grasslands may respond differently to those practices. The study aimed to investigate the effect of fertilisation type (farm yard manure (FYM) and NPK fertilisation) and the timing of the first regrowth harvest of meadow sward (ten harvest dates) on the lignin and structural carbohydrates of three dicotyledonous meadow plants: Taraxacum officinale F.H. Wigg., Achillea millefolium L. and Lotus corniculatus L. Plant material was harvested from 28 Apr until 26 Jun at 7-day intervals and analysed for cellulose (CL), hemicellulose (HCL), and acid detergent lignin (ADL). The levels of neutral detergent fibre (NDF), acid detergent fibre (ADF), and ADL were measured using near-infrared spectroscopy (NIRS) with a NIRFlex N-500 device. Cellulose was calculated as the difference between ADF and ADL, while HCL was calculated by subtracting ADF from NDF. T. officinale had the lowest HCL (average 65.5 g∙kg−1 DM) and ADL content (47.1 g∙kg−1 DM) while A. millefolium had the highest CL content (266.5 g∙kg−1 DM) and ADL (52.3 g∙kg−1 DM). In contrast, L. corniculatus accumulated the highest HCL (104.5 g∙kg−1 DM) and the lowest CL content (246.1 g∙kg−1 DM). An increase in all studied parameters content was observed with later harvest dates. On average, plants fertilised with FYM contained lower amounts of structural carbohydrates and ADL compared to those fertilised with NPK.

The aim of the study was to compare the antioxidant activity and polyphenol content in extracts prepared from freeze-dried leaves of three apple cultivars: Ligol, Gala, and Gloster, using different solvents and extraction methods. The content of total polyphenols was determined using the Folin–Ciocâlteu reagent method, and a qualitative and quantitative analysis of polyphenols was performed using the HPLC method. The antioxidant capacity of the extracts was determined using the DPPH radical method. The colour parameters (in the CIEL*a*b system) of the obtained extracts were also determined. The antioxidant activity of apple leaf extracts increased with increasing polyphenol content. Water–alcoholic extracts from apple leaves were characterised by a significantly higher antioxidant capacity and polyphenol content in comparison with water extracts. The best solvent was a mixture of water and methanol (80%). Among the phenolic compounds identified in the extracts, the most common was phloridzin. The highest content of phloridzin (105.0 mg/1 g of dry weight) was found in water–methanol extracts from the leaves of the Ligol variety obtained with ultrasound-assisted extraction. The extracts with the highest antioxidant activity (131.2 μmol of Trolox/1 g of dry weight) and polyphenol content (81.9 mg GAE/1 g of dry weight) were water–methanol from the leaves of the Ligol cultivar, obtained by shaking them with a solvent.

Melica uniflora Retz., commonly known as wood melick, is a grass species that is native to most of Europe. Melica uniflora grows in hardwood forests near Fagus species, providing vital food and shelter for forest wildlife. The nutritional status of wood melick is not sufficiently recognized. The study aims to identify the intrapopulation variability of Melica uniflora plants collected from natural forest habitats in Poland in terms of nutritional status variability in relation to stage development and the course of weather conditions. The research was conducted for two consecutive years: 2021 and 2022, in the area of the Ślęża Massif, near the town of Sobótka in Lower Silesia voivodeship (Poland). The material for analyses was collected from 10 natural forest sites twice: in July (I) and October (II). The content of nutritive components: crude protein (CP), crude ash (CA), neutral detergent fiber (NDF), acid detergent fiber (ADF), acid detergent lignin (ADL), and water-soluble carbohydrates (WSC) was evaluated. Relative feed value (RFV), dry matter digestibility (DDM), dry matter intake (DMI), cellulose (CL), and hemicellulose (HCL) content were calculated based on ADF and NDF. Melica uniflora plants contained 75.2 g·kg⁻¹ DM of CP, 290.6 g·kg⁻¹ DM of CF, 120.0 g·kg⁻¹ DM of CA, and 25.9 g·kg⁻¹ DM of WSC. The content of NDF was 637.6 g·kg⁻¹ DM, ADF 407.5 g·kg⁻¹ DM, and ADL 58.0 g·kg⁻¹ DM. The nutritional status of wood melick depended on the course of weather conditions in the following years and its location, which changed during the growing season. Plants collected in the first year of the study contained more CL, NDF, and ADF fractions and less CA, ADL, and WSC. Melica uniflora plants harvested in June were characterized by higher CP (102.1 g·kg⁻¹ DM) and WSC (30.1 g·kg⁻¹ DM) content and lower content of remaining nutrients. It can be concluded that Melica uniflora plants can be a valuable source of these nutrients in the forage of forest animals.